Update version of owlapi and fixed issues introduced in previous pr

dgarijo · dgarijo · commit e3fab26509fa · 2026-04-01T16:44:46.000+02:00
diff --git a/pom.xml b/pom.xml
@@ -10,7 +10,7 @@
     </parent>
     <groupId>es.oeg</groupId>
     <artifactId>fair_ontologies</artifactId>
-    <version>0.3.1</version>
+    <version>0.3.2</version>
     <packaging>jar</packaging>
     <name>fair_ontologies</name>
     <description>FOOPS!: An Ontology Pitfall scanner for the FAIR principles</description>
@@ -79,10 +79,15 @@
         </dependency>
 
         <!-- OWL API-->
-        <dependency>
+        <!--<dependency>
             <groupId>net.sourceforge.owlapi</groupId>
             <artifactId>owlapi-distribution</artifactId>
             <version>5.1.14</version>
+        </dependency>-->
+        <dependency>
+            <groupId>net.sourceforge.owlapi</groupId>
+            <artifactId>owlapi-apibinding</artifactId>
+            <version>5.5.0</version>
         </dependency>
 
     </dependencies>
diff --git a/src/main/java/entities/Ontology.java b/src/main/java/entities/Ontology.java
@@ -21,12 +21,16 @@
 import fair.Constants;
 import fair.Utils;
 import org.jsoup.nodes.Document;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.StreamDocumentSource;
 import org.semanticweb.owlapi.model.*;
 import org.semanticweb.owlapi.search.EntitySearcher;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import server.FileTooLargeException;
 
+import java.io.File;
+import java.io.FileInputStream;
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
@@ -65,28 +69,29 @@ public class Ontology {
     private final ArrayList<String> supportedMetadata;
     private final ArrayList<String> reusedMetadataVocabularies;
     private final ArrayList<String> reusedVocabularies;
-    List<OWLImportsDeclaration> importedVocabularies;
+    List<IRI> importedVocabularies;
     private final ArrayList<String> termsWithLabel;
     private final ArrayList<String> terms; // all terms
     private final ArrayList<String> termsWithDescription;
     private boolean isSKOS = false;
 
     /**
-     *
+     * Ontology class constructor
      * @param o ontology path or URI
      * @param isFromFile flag to indicate whether the ontology should be loaded from file or URL
      * @param tmpFolder temporary folder where to store the downloaded ontology
      */
     public Ontology(String o, boolean isFromFile, Path tmpFolder) throws FileTooLargeException {
         supportedMetadata = new ArrayList<>();
+        importedVocabularies = new ArrayList<>();
         reusedMetadataVocabularies = new ArrayList<>();
         reusedVocabularies = new ArrayList<>();
         termsWithLabel = new ArrayList<>();
         termsWithDescription = new ArrayList<>();
         terms = new ArrayList<>();
         //Download ontology (any serialization)
         try {
-            this.ontologyModel = Utils.loadModelToDocument(o, isFromFile, tmpFolder.toString());
+            this.loadModelToDocument(o, isFromFile, tmpFolder.toString());
             if (this.ontologyModel != null && this.ontologyModel.getOntologyID().getOntologyIRI().isPresent()) {
                 this.ontologyURI = this.ontologyModel.getOntologyID().getOntologyIRI().get().toString();
             } 
@@ -456,8 +461,10 @@ private void completeMetadata(OWLAnnotation a) {
     private void getOntologyCoverage(){
         //metadata vocabularies
         this.ontologyModel.annotations().forEach(this::checkNamespaces);
-        //imports
-        this.importedVocabularies = this.ontologyModel.importsDeclarations().collect(Collectors.toList());
+        // imports -> they are loaded when the ontology is loaded.
+        // due to slow imports, we have disabled loading of imports
+        //this.importedVocabularies = this.ontologyModel.importsDeclarations().collect(Collectors.toList());
+
         //vocabulary reuse
         logger.info("Extracting namespaces, labels, descriptions");
         if(isSKOS) {
@@ -643,7 +650,7 @@ public ArrayList<String> getReusedMetadataVocabularies() {
         return reusedMetadataVocabularies;
     }
 
-    public List<OWLImportsDeclaration> getImportedVocabularies() {
+    public List<IRI> getImportedVocabularies() {
         return importedVocabularies;
     }
 
@@ -727,4 +734,71 @@ public String getNamespaceUri(){
         if (namespaceUri.isEmpty()) return "unknown";
         else return namespaceUri;
     }
+
+    /**
+     * Method that will download the ontology to process with FOOPS!
+     * Note: lazy loading of imports is implemented (making them fail).
+     *
+     * @param isFromFile boolean to indicate whether the ontology is from file or from URI.
+     */
+    private void loadModelToDocument(String pathOrURI,boolean isFromFile, String downloadFolder) throws Exception {
+        String ontologyPath = pathOrURI;
+        if (!isFromFile) {
+            ontologyPath = downloadFolder + File.separator + "ontology";
+            Utils.downloadOntology(pathOrURI, ontologyPath);
+        }
+        logger.info("Loading ontology ");
+        File ontologyFile = new File(ontologyPath);
+        // if ontology is bigger than 50 MB, we do not process it
+        if (ontologyFile.length() > Constants.MAX_ONTOLOGY_SIZE) {
+            throw new FileTooLargeException("File is larger than maximum allowed (50 MB): " );
+        }
+        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+
+        // --- BLOCK TO PREVENT IMPORTS IN OWLAPI 5.5.0 ---
+        manager.getIRIMappers().add(iri -> {
+            if (!iri.equals(IRI.create(pathOrURI))) {
+                logger.warn("Blocking import: " + iri);
+                //record the imported vocabulary for later purposes
+                this.importedVocabularies.add(iri);
+                return IRI.create("file:///dev/null");
+                // we make the import fail along with MissingImportHandlingStrategy.SILENT
+                // and follow redirects set to false
+            }
+            ////return IRI.create("urn:dummy:" + iri);
+            return null;
+        });
+
+        // -----------------------------------------------------
+
+        //this is for debugging purposes, to check that the imports are being blocked.
+        // but add helped information about the loading process
+        manager.addOntologyLoaderListener(new OWLOntologyLoaderListener() {
+            @Override
+            public void startedLoadingOntology(OWLOntologyLoaderListener.LoadingStartedEvent event) {
+                if (!event.getDocumentIRI().equals(IRI.create(pathOrURI))) {
+                    logger.debug("Skipping import: " + event.getDocumentIRI());
+                } else {
+                    logger.debug("Loading main ontology: " + event.getDocumentIRI());
+                }
+            }
+
+            @Override
+            public void finishedLoadingOntology(OWLOntologyLoaderListener.LoadingFinishedEvent event) {
+                logger.info("Finished loading: " + event.getDocumentIRI());
+            }
+        });
+
+
+        OWLOntologyLoaderConfiguration loadingConfig = new OWLOntologyLoaderConfiguration();
+        loadingConfig = loadingConfig.setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT);
+        loadingConfig = loadingConfig.setFollowRedirects(false);
+
+        logger.info("Parsing type: "+loadingConfig.isStrict());
+
+        this.ontologyModel = manager.loadOntologyFromOntologyDocument(
+                new StreamDocumentSource(new FileInputStream(ontologyFile), IRI.create(pathOrURI)),
+                loadingConfig
+        );
+    }
 }
diff --git a/src/main/java/entities/checks/Check_VOC1_VocabReuseMetadata.java b/src/main/java/entities/checks/Check_VOC1_VocabReuseMetadata.java
@@ -44,7 +44,7 @@ public void check(){
         super.check();
         this.reference_resources = new ArrayList<>();
         reference_resources = ontology.getReusedMetadataVocabularies();
-        if(reference_resources.size()>0){
+        if(!reference_resources.isEmpty()){
             this.total_passed_tests++;
             status = Constants.OK;
             explanation = Constants.VOC1_EXPLANATION_OK;
@@ -53,7 +53,7 @@ public void check(){
             explanation = Constants.VOC1_EXPLANATION_ERROR;
         }
         //to avoid returning empty lists
-        if(reference_resources.size() == 0){
+        if(reference_resources.isEmpty()){
             reference_resources = null;
         }
     }
diff --git a/src/main/java/entities/checks/Check_VOC2_VocabReuse.java b/src/main/java/entities/checks/Check_VOC2_VocabReuse.java
@@ -21,6 +21,7 @@
 import entities.Ontology;
 import fair.Constants;
 import org.apache.tomcat.util.bcel.Const;
+import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLImportsDeclaration;
 
 import java.util.ArrayList;
@@ -46,11 +47,11 @@ public void check(){
         super.check();
         try{
             //first, if there are imports, we are done.
-            List<OWLImportsDeclaration> imports = this.ontology.getImportedVocabularies();
+            List<IRI> imports = this.ontology.getImportedVocabularies();
             this.reference_resources = new ArrayList<>();
             if (!imports.isEmpty()) {
-                for (OWLImportsDeclaration imp:imports){
-                    reference_resources.add(imp.getIRI().getIRIString());
+                for (IRI imp:imports){
+                    reference_resources.add(imp.getIRIString());
                 }
                 total_passed_tests ++;
                 status = Constants.OK;
diff --git a/src/main/java/fair/Utils.java b/src/main/java/fair/Utils.java
@@ -34,79 +34,13 @@
 import java.nio.file.Files;
 import java.nio.file.Paths;
 import java.nio.file.StandardCopyOption;
+import java.util.ArrayList;
+import java.util.Optional;
 
 public class Utils {
 
     private static final Logger logger = LoggerFactory.getLogger(Utils.class);
 
-    /**
-     * Method that will download the ontology to document with Widoco.
-     *
-     * @param isFromFile boolean to indicate whether the ontology is from file or from URI.
-     */
-    public static OWLOntology loadModelToDocument(String pathOrURI,boolean isFromFile, String downloadFolder) throws Exception {
-        String ontologyPath = pathOrURI;
-        if (!isFromFile) {
-            ontologyPath = downloadFolder + File.separator + "ontology";
-            downloadOntology(pathOrURI, ontologyPath);
-        }
-        logger.info("Loading ontology ");
-        File ontologyFile = new File(ontologyPath);
-        // if ontology is bigger than 50 MB, we do not process it
-        if (ontologyFile.length() > Constants.MAX_ONTOLOGY_SIZE) {
-            throw new FileTooLargeException("File is larger than maximum allowed (50 MB): " );
-        }
-        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
-
-        // --- BLOCK TO PREVENT IMPORTS IN OWLAPI 5.1.14 ---
-        manager.getIRIMappers().add(iri -> {
-            if (!iri.equals(IRI.create(pathOrURI))) {
-                System.out.println("Blocking import: " + iri);
-                return IRI.create("file:///dev/null"); 
-                // we make the import fail along with MissingImportHandlingStrategy.SILENT
-                // and follow redirects set to false
-            }
-            return null;
-        });
-        // -----------------------------------------------------
-
-        //this is for debugging purposes, to check that the imports are being blocked.
-        // but add helped information about the loading process
-        manager.addOntologyLoaderListener(new OWLOntologyLoaderListener() {
-            @Override
-            public void startedLoadingOntology(OWLOntologyLoaderListener.LoadingStartedEvent event) {
-                if (!event.getDocumentIRI().equals(IRI.create(pathOrURI))) {
-                    System.out.println("Skipping import: " + event.getDocumentIRI());
-                } else {
-                    System.out.println("Loading main ontology: " + event.getDocumentIRI());
-                }
-            }
-
-            @Override
-            public void finishedLoadingOntology(OWLOntologyLoaderListener.LoadingFinishedEvent event) {
-                System.out.println("Finished loading: " + event.getDocumentIRI());
-            }
-        });
-
-
-        OWLOntologyLoaderConfiguration loadingConfig = new OWLOntologyLoaderConfiguration();
-        loadingConfig = loadingConfig.setMissingImportHandlingStrategy(MissingImportHandlingStrategy.SILENT);
-        loadingConfig = loadingConfig.setFollowRedirects(false);
-
-        // only works for owlpai 6.x, but not for 5.1.14, which is the one we are using in the tests
-        // loadingConfig = loadingConfig.setLoadImports(false);
-        // loadingConfig = loadingConfig.setProcessImports(false); 
-
-        logger.info("Parsing type: "+loadingConfig.isStrict());
-        
-        OWLOntology ontology = manager.loadOntologyFromOntologyDocument(
-            new StreamDocumentSource(new FileInputStream(ontologyFile), IRI.create(pathOrURI)), 
-            loadingConfig
-        );
-
-        return ontology;
-    }
-
     public static void addAnnotationToOntology(OWLDataFactory df, OWLOntology o,IRI ontoURI, String propertyURI, String value){
         OWLAnnotationProperty predicate = df.getOWLAnnotationProperty(IRI.create(propertyURI));
         OWLAnnotation annotation = null;

Original file line number	Diff line number	Diff line change
`@@ -44,7 +44,7 @@ public void check(){`
`44`	`44`	`super.check();`
`45`	`45`	`this.reference_resources = new ArrayList<>();`
`46`	`46`	`reference_resources = ontology.getReusedMetadataVocabularies();`
`47`		`- if(reference_resources.size()>0){`
	`47`	`+ if(!reference_resources.isEmpty()){`
`48`	`48`	`this.total_passed_tests++;`
`49`	`49`	`status = Constants.OK;`
`50`	`50`	`explanation = Constants.VOC1_EXPLANATION_OK;`
`@@ -53,7 +53,7 @@ public void check(){`
`53`	`53`	`explanation = Constants.VOC1_EXPLANATION_ERROR;`
`54`	`54`	`}`
`55`	`55`	`//to avoid returning empty lists`
`56`		`- if(reference_resources.size() == 0){`
	`56`	`+ if(reference_resources.isEmpty()){`
`57`	`57`	`reference_resources = null;`
`58`	`58`	`}`
`59`	`59`	`}`